#! /usr/bin/env python # -*- coding: utf-8 -*- ############################################################################## ## DendroPy Phylogenetic Computing Library. ## ## Copyright 2010-2015 Jeet Sukumaran and Mark T. Holder. ## All rights reserved. ## ## See "LICENSE.rst" for terms and conditions of usage. ## ## If you use this work or any portion thereof in published work, ## please cite it as: ## ## Sukumaran, J. and M. T. Holder. 2010. DendroPy: a Python library ## for phylogenetic computing. Bioinformatics 26: 1569-1571. ## ############################################################################## """ Wrappers for interacting with ITOL. """ import os import sys import tempfile if sys.version_info.major < 3: from urllib import urlencode from urllib import urlopen else: from urllib.parse import urlencode from urllib.request import urlopen from urllib import request import zipfile try: import zlib COMPRESSION_TYPE = zipfile.ZIP_DEFLATED except: COMPRESSION_TYPE = zipfile.ZIP_STORED import dendropy from dendropy.utility import textprocessing from dendropy.utility import urlio from dendropy.utility import error class ItolService(object): DISPLAY_MODE_NORMAL = 1 DISPLAY_MODE_CIRCULAR = 2 DISPLAY_MODE_UNROOTED = 3 RENDER_PARAM_NAMES = set([ "newick_format", "display_mode", "tree_x", "tree_y", "vertical_shift_factor", "horizontal_scale_factor", "current_font_size", "current_font_name", "current_font_style", "leaf_sorting", "label_display", "align_labels", "label_shift", "dashed_lines", "ignore_branch_length", "slanted_normal", "arc", "rotation", "normal_rotation", "unrooted_rotation", "line_width", "default_branch_color", "default_label_color", "inverted", "circle_size_inverted", "range_mode", "include_ranges_legend", "ranges_legend_title", "internal_marks", "internal_scale", "internalScale1", "internalScale2", "internalScale1Color", "internalScale2Color", "branchlength_display", "branchlength_label_size", "branchlength_label_position", "branchlength_label_sci", "branchlength_label_rounding", "branchlength_label_age", "metadata_source", "bootstrap_display", "bootstrap_type", "bootstrap_symbol", "bootstrap_symbol_min", "bootstrap_symbol_max", "bootstrap_symbol_position", "bootstrap_symbol_color", "bootstrap_slider_min", "bootstrap_slider_max", "bootstrap_label_position", "bootstrap_label_size", "bootstrap_label_sci", "bootstrap_label_rounding", "bootstrap_width_min", "bootstrap_width_max", "bootstrap_min_color", "bootstrap_use_mid_color", "bootstrap_mid_color", "bootstrap_max_color", "datasets_visible", ]) def __init__(self, **kwargs): """ Keyword Arguments ----------------- newick_format: int Possible value: ID. Only used when export format is set to newick. If specified, internal node IDs will be included in exported Newick trees. display_mode: int Possible values: 1,2 or 3 (1=normal, 2=circular, 3=unrooted) tree_x: int Tree will be shifted horizontally by this value, positive or negative (value in pixels) tree_y: int Tree will be shifted vertically by this value, positive or negative (value in pixels) vertical_shift_factor: int Vertical tree scaling factor (positive number) horizontal_scale_factor: int Horizontal tree scaling factor (positive number) current_font_size: int Main label font size in pixels (integer >= 9) current_font_name: int Possible values: 'Arial', 'Courier', 'Courier New', 'Verdana', 'Impact', 'Georgia', 'Times New Roman' or 'Monotype Corsiva' current_font_style: int Possible values: 'normal', 'bold' or 'bold italic' leaf_sorting: int Possible values: 1 or 2 (1=normal sorting, 2=no sorting) label_display: int Possible values: 0 or 1 (0=hide labels, 1=show labels) align_labels: int Possible values: 0 or 1 (0=labels not aligned, 1=labels aligned) label_shift: int Amount to shift the leaf labels (positive or negative, in pixels) dashed_lines: int Display dashed lines connecting branches to leaf labels. Possible values: 0 or 1 (0=hide lines, 1=display lines) ignore_branch_length: int Possible values: 0 or 1 slanted_normal: int Display tree in slanted (triangular) mode. Note that display_mode must be 1. Possible values: 0 or 1 arc: int Angle of the display arc for the circular tree (in degrees, a number between 0 and 360) rotation: int Rotation angle for circular tree (in degrees, a number between 0 and 360) normal_rotation: int Rotation angle for normal tree (in degrees, a number between 0 and 360) unrooted_rotation: int Rotation angle for unrooted tree (in degrees, a number between 0 and 360). line_width: int Width of tree lines (in pixels). default_branch_color: str Default color of tree's branches (hex, RGB or RGBA notation). default_label_color: str Default color of tree's labels (hex, RGB or RGBA notation). inverted: int Inverted display (only for circular and normal mode). Possible values: 0 or 1. circle_size_inverted: int For inverted circular display only. Internal radius will be increased by this amount (value in pixels) range_mode: int Colored ranges display style. Possible values: 0,1 or 2 (0=off, 1=cover labels only, 2=cover full clades)< include_ranges_legend: int Include colored ranges legend. Possible values: 0 or 1. ranges_legend_title: str Title of the colored ranges legend. internal_marks: int Draw circles to mark the location of internal nodes. Possible values: 0, 1 or 2 (0=Do not display, 1=Display on nodes with one child, 2=Display always). internal_scale: int Draw internal tree scale. Possible values: 0 or 1. internalScale1: int Repeat value for the first set of internal scale lines (branch length value) internalScale2: int Repeat value for the second set of internal scale lines (branch length value). internalScale1Color: str Color for the first set of internal scale lines (hex, RGB or RGBA). internalScale2Color: str Color for the second set of internal scale lines (hex, RGB or RGBA). branchlength_display: int Display branch length text labels on branches (possible values: 0 or 1). branchlength_label_size: int Font size for the branch length labels (in pixels, integer >= 0) branchlength_label_position: int Position of the branch length labels along the branch (in percent, default is 50%). branchlength_label_sci: int Display branch length labels in scientific notation (if set to 1). branchlength_label_rounding Round branch length labels to this number of decimals (integer >= 0). branchlength_label_age Display node age instead of raw branch length values (if set to 1). metadata_source: str Which metadata source to use for bootstrap display options (default: 'bootstrap', other possible options depend on the data in the tree). bootstrap_display: int Display metadata values (possible values: 0 or 1). bootstrap_type: int Type of metadata display. Possible values: 1, 2, 3 or 4 (1=Symbol, 2=Text label, 3=Branch color and 4=Branch width. bootstrap_symbol: int Symbol used to display metadata values. Possible values: 1, 2, 3 or 4 (1=Circle, 2=Triangle, 3=Square and 4=Star). bootstrap_symbol_min: int Minimum size for the metadata symbol (in pixels). bootstrap_symbol_max: int Maximum size for the metadata symbol (in pixels). bootstrap_symbol_position: int Position of the metadata symbol along the branch (in percent, default is 50%). bootstrap_symbol_color: str Bootstrap symbol color (hex, RGB or RGBA). bootstrap_slider_min: int Minimum metadata value to display. bootstrap_slider_max: int Maximum metadata value to display. bootstrap_label_position: int Position of the metadata text label along the branch (in percent, default is 50%). bootstrap_label_size: int Font size for the metadata text labels (in pixels, integer >= 9). bootstrap_label_sci: int Display metadata labels in scientific notation (if set to 1). bootstrap_label_rounding: int Round metadata labels to this number of decimals (integer >= 0). bootstrap_width_min: int Branch width for minimum metadata value (in pixels), when bootstrap_type=4. bootstrap_width_max: int Branch width for maximum metadata value (in pixels), when bootstrap_type=4. bootstrap_min_color: int Branch color for minimum metadata value (hex, RGB or RGBA), when bootstrap_type=3. bootstrap_use_mid_color: int Use a three color gradient for metadata branch colors (possible values: 0 or 1). bootstrap_mid_color: str Branch color for midpoint metadata value (hex, RGB or RGBA), when bootstrap_type=3 and bootstrap_use_mid_color=1. bootstrap_max_color: str Branch color for maximum metadata value (hex, RGB or RGBA), when bootstrap_type=3. datasets_visible: int Comma delimited list of datasets to display (starting with 0, e.g. datasets_visible=0,2,5). """ self._base_upload_url = "https://itol.embl.de/batch_uploader.cgi" self._base_download_url = "https://itol.embl.de/batch_downloader.cgi" self._headers = {"Content-type": "application/x-www-form-urlencoded", "Accept": "text/plain"} self._render_params = {} for k, v in kwargs: setattr(self, k, v) def __setattr__(self, name, value): if name in ItolService.RENDER_PARAM_NAMES: if value is None: try: del self._render_params[name] except KeyError: pass else: self._render_params[name] = value object.__setattr__(self, name, value) def read_remote(self, tree_id, result_format): """ Executes query and returns binary result. """ params_d = { "tree": tree_id, "format": result_format, } params_d.update(self._render_params) params = urlencode(params_d) req = request.Request( self._base_download_url, params.encode("ascii"), self._headers) response = urlopen(req) result = response.read() return result def download(self, dest, tree_id, result_format): """ Executes query and writes binary result to 'dest'. Examples -------- :: from dendropy.interop import itol itol_service = itol.ItolService() itol_service.display_mode = 1 itol_service.label_display = 0 itol_service.ignore_branch_length = 1 itol_service.normal_rotation = 90 itol_service.slanted_normal = 1 itol_service.line_width = 13 itol_service.internal_scale = 0 result_format = "pdf" # "png", "svg", etc. itol_service.download( dest="x1.{}".format(result_format), tree_id=709552230231221546743590, result_format=result_format,) """ result = self.read_remote( tree_id=tree_id, result_format=result_format,) if isinstance(dest, str): dest = open(dest, "wb") with dest: dest.write(result) def upload(self, tree): """ Uploads a tree to iTOL. Examples -------- :: import dendropy from dendropy.utility import itol tree = dendropy.Tree.get(data="[&R] (A1,(B2,(C3,(D4,E5))));", schema="newick") itol_service = ItolService() tree_id = itol_service.upload(tree) print(tree_id) """ import requests with tempfile.TemporaryDirectory() as temp_dirname: zf_path = os.path.join(temp_dirname, "data.zip") tree_str = tree.as_string(schema="newick") zf = zipfile.ZipFile(zf_path, mode="w", compression=COMPRESSION_TYPE) # zf = zipfile.ZipFile(zf_path, mode="w") with zf: zf.writestr("tree.tree", tree_str,) with open(zf_path, "rb") as zf: files = {"zipFile": open(zf_path, "rb")} response = urlio.post_request( url=self._base_upload_url, files=files) response_text = response.text if "SUCCESS" not in response_text: raise error.ExternalServiceError( service_name="iTOL", invocation_command=self._base_upload_url, service_input="", returncode=-1, stdout=response_text, stderr="") response_lines = [row for row in response_text.split("\n") if row] warnings = response_lines[0:-1] tree_id = response_lines[-1].split()[1] return tree_id def render_tree(self, tree, dest, result_format,): """ Renders a tree using the iTOL web service. Examples -------- :: itol_service = ItolService() result_format = "pdf" tree = dendropy.Tree.get(data="[&R] (A1,(B2,(C3,(D4,E5))));", schema="newick") itol_service.render_tree( tree=tree, dest="sample.{}".format(result_format), result_format=result_format,) """ tree_id = self.upload(tree) self.download( dest=dest, tree_id=tree_id, result_format=result_format,) return tree_id